The V3-V4 region of the bacterial 16S rRNA in the intestinal contents of three commercial fish species (Larimichthys crocea, Larimichthys polyactis and Trichiurus lepturus) from the central and southern East China Sea were sequenced in an attempt to understand the intestinal microbial diversity (IMD) and community structure of the intestinal microbiota in these populations collected in spring and autumn.